MPI Toolbox for Octave (MPITB) 
 

Authors:
  • Javier Fernández Baldomero
  • Mancia Anguita

What is MPITB?:
Octave Linux users in a cluster with several PCs can use MPITB in order to call MPI library routines from within the Octave environment.
Parallel applications can be launched using mpirun, Octave variables can be sent/recvd, etc. A set of demos of increasing difficulty level are provided for an easier learning curve: Hello, Pi, PingPong, Mandelbrot, NPB/EP, Spawn, Wavelets...
Although using mpirun is easier for most applications, in some circumstances it might be convenient that new processes be spawned from a master Octave session using MPI_Comm_spawn(_multiple). Thanks to Octave's eval command, commands for remote execution may be passed as strings to the desired Octave computing instance, and the results may be sent back to the Octave host instance (master session). Several protocols to facilitate these procedures are suggested in the startups and utils subdirs.
Some citations to MPITB have been collected here (papers, conferences, labs, etc.) Last update Nov'08.
 (17/Jul/07) MPITB precompiled for Octave-2.9.12 and (LAM-7.1.3 or Open-MPI-1.2.3). The Spawn demos are not completely supported under OMPI yet, but all mpirun demos work.
 (20/May/08) New PelicanHPC release, including precompiled MPITB with Octave-3.0.1 and OMPI-1.2.6.
 (12/Jun/08) MPITB ported to MPICH on a BlueGene/L supercomputer called Hebb (5.7 TF, 13.7TB, Top500 379@2007) in KTH PDC, Sweden.
 (Oct/08) MPITB ported to BlueGene/P as well. Document mentions peak 13.93TF, linpack 11.11TF, must be Schrödinger (Top500 307@2008).
 (3/Apr/09) MPITB tutorial file (and Pi demo) ported to NSP. See Toolboxes. Read post #6 by jpc in this thread (01/Oct/08).
 (17/Apr/09) MPITB in use at Lisa64 (11.5TF, 25TB, Top500 140-435@2005/06) in SARA, Netherland.

 Last users search & update Apr'09 (lisa64)
 

Sites with links to MPITB:



Last links search & update Apr'09 (SARA)

Open MPI Home Page ( - FAQ - Building - Compiling MPI apps - #16 other bindings)

LAM Home Page ( - MPI Applications ).

Wikipedia > GNU Octave > Links > last link
Wikipedia > MPI > Links > near the end

GNU Octave > Wiki > Who Uses Octave > Gianvito's experience (2nd)



Pelican-HPC is the new sequel to Parallel-Knoppix after v2.8 release
(May/20/2008 MPITB precompiled and working out-of-the-box with Octave-3.0.1 and OpenMPI-1.2.6)


Parallel-Knoppix Home Page (64-bit operation confirmed)


SARA ( > Systems > lisa )

 ( software > various > MPITB ) (MPITB at 11.5TF in a Top500 system!)


Kungliga Tekniska Högskolan Sweden KTH ( > ParallelDatorCentrum > Systems Support > Computers > hebb > Octave on BlueGene > )

MPITB and Octave on BlueGene/L (MPITB on BG/L in a Top500 system!)



VL-e (Virtual Laboratory for E-Science) > POC (Proof-Of-Concept) > R1, R2, R3 proposal



UIC (University of Illinois at Chicago > Mathematics Dept. (MCSC) > )
Yun Guan Home Page > Resources > Technologies
See also > Research > Software / Publications


CICA (Centro Informático Científico de Andalucía > Software > Cálculo OpenSource > ) Octave


Technological Education Institute of Messolonghi (TEIMES > EPDO > HPCS Lab) WebLinks


Debian Octave Group ( Debian > Development > Projects > Alioth > pkg-octave > DOG )

MPITB mentioned in section "Other interesting Octave stuff" at the end of the page


Dalhousie University ( > Academic Study > Faculties > Science > Departments (correct) > Earth Sciences (corr) > Website > Surface/Marine/Environmental > Lawrence Plug > Surface Processes / Pattern Lab (corr) > Tools > Clusters and Parallel Computing page)


Geordie McBain's Octave page ( University of Sydney > Engineering > Aerospace - Mechanical Engr. > Research > Areas > Fluid Dynamics >)

Geordie McBain > List of Computing links > Octave > Parallelizing Octave



Russel Luke's Parallel MATLAB Page ( University of Delaware > Academic&Research > Departments > Matematical Sciences > People > Faculty > Luke, D.R. > Home Page > Research > Parallel MATLAB and Octave > Parallel Octave)

 

Index:

Features:

Source code included.
Supports all octave types from cell up to struct (type "typeinfo" at octave prompt). Support for all Octave ND arrays and integer types. Reduce operators _BAND/OR/XOR also supported on the integer types.
Support for the new (2.9.x) sparse types.
Can be recompiled for x86, x86_64, ia64 architectures. The main include file mpitb.h detects the architectural GCC symbol and changes #defines accordingly.
Supports all MPI-1.2 calls, except for MPI_Pcontrol, MPI_Op_create, MPI_Op_free, and those related to derived datatypes (MPI_Type_*). They're meaningless under Octave, which has no corresponding functionality.
Also included some MPI-2.0 calls: the Info object (MPI_Info_*) and Spawn (MPI_Comm_spawn[_multiple], _Comm_get_parent, _Open/Close_port, _Comm_accept/connect/disconnect, _[Un]Publish/Lookup_name).
Demo subdirs: Hello, Pi, PingPong, Mandelbrot, NPB/EP, Spawn, Wavelets. See the README included on each one.
Help docstring for all interfaced MPI calls, extracted from LAM/MPI man pages, which in turn were initially based on MPICH man pages (thanks to all)
Utility subdir, with protocol commands (such as "LAM_Init", "Octave_Spawn", "NumCmds_Send") and instrumentation commands (such as "time_stamp" and "look_instr") which can be useful if you need to use MPI_Comm_spawn or you want to assess where time is spent in your sequential application. See the examples in the Spawn and Wavelets subdirs to get a hint on their possible uses.
 

Requirements:



MPITB needs a working LAM or Open-MPI dynamically linked (shared libraries) installation. Same version on all nodes. This requirement is frequently overlooked. See long descriptions under "Requirements" and "Installing".


MPITB also needs a working Octave installation (with DLD support) on each node on which you want to spawn an Octave process. Same version on all nodes. MPITB should work out-of-the-box if you use the same Octave version in your cluster (compared to the tarball), and similar enough LAM or OMPI configure switches. See long descriptions under "Requirements" and "Installing".


Please check the MD5 sum before installing.
Tested under several Intel/AMD Linux compiling environments, such as:
  • i686 Pentium II 333MHz, RedHat 8.0/9.0, glibc-2.3.2 (gcc 3.2.2/7), Octave 2.1.50/57/60, LAM 7.0.2/4
  • i686 Athlon MP 2400+ (biproc), Fedora Core 6, glibc-2.5 (gcc 4.1.2), Octave 3.0.0, LAM 7.1.4, OMPI 1.2.6
  • i686 Xeon 2.66GHz (tetraproc), Red Hat Enterprise Linux ES release 4, glibc-2.3.4 (gcc 3.4.3), Octave 2.1.73, LAM 7.1.2
  • ia64 Itanium II 1GHz (biproc), HP-XC 2.0 LHPC 3, glibc-2.3.2 (gcc-3.2.3), Octave-2.1.72, LAM-7.1.1
  • x86-64 Pentium D 3.2GHz (tetraproc), Fedora Core 5. gcc-4.1.0, Octave-2.1.73, LAM-7.1.2
The main include file mpitb.h detects the architectural GCC symbol and changes #defines accordingly




Downloads:



17/Jul/07: precompiled for Oct-2.9.12 and both LAM-7.1.3 and Open-MPI-1.2.3
  mpitb-beta-FC6-OCT2912-LAM713-OMPI123.tar.bz2 (5062419bytes) (sum file oct2912lam713ompi123sum)

PDFs comparing performance in Pi and PingPong subdirs... It seems a good idea to gradually move towards OMPI, not only for performance but also for maintainability.
(May/08) the beta works with octave-3.0.1


Older versions indexed under "Downloads"




Installing:



Make sure you have a shared-libraries LAM or OMPI installation available in all nodes in your cluster. 
Make sure your octave executable has been compiled with DLD support, and it's the same version in all cluster nodes.
Make sure the octave binary you wish/choose is in your search path on each node as well as the desired/chosen LAM/OMPI binaries. Also double-check that the corresponding LAM/OMPI libraries (same version / configure switches as the chosen LAM/OMPI binaries) are included in your LD_LIBRARY_PATH.
That's frequently overlooked. See a long description under "Installing".
A shared (among nodes, cluster-wide) HOME is strongly advised, as well as installing there all the required software. That way, you won't depend on anybody else. If not, you may need to play with your configuration and/or ask your sysadmin until the above requirements (or equivalent ones for non-ssh clusters) are met.


  • Unzip & untar the toolbox. Recomended location is under ~/octave,  so a new directory ~/octave/mpitb appears.
  • Enter the new mpitb subdir, read/edit the lam-bhost.def file to describe your cluster and lamboot your LAM (not applicable if using OMPI)
  • Run there octave and try some MPITB command such as MPI_Initialized or MPI_Init. It might work out-of-the-box.
  • If not, your octave version or LAM/OMPI configure switches are probably too different and MPITB needs a remake: just enter the src subdir, make sure the commands "octave-config", "mkoctfile", "(lam/ompi_)info" and "mpiCC" all work and correspond to your desired Octave / LAM/OMPI --enable-shared versions, and type "make".
  • Read the README file for more detailed instructions. Read the Makefile to understand why those 4 commands are required.
  • Work through the demos to learn to use the toolbox. The recommended order is Hello, Pi, PingPong, Mandelbrot, NPB/EP.
  • Remember to halt LAM when you leave (also not much of a problem if you let the daemons there)







Community:
  • This section was started to keep track of Michael Creel's work with MPITB. Initially, there were just a couple of acknowledgements in the "Features" section.
  • There is also a Parallel-Knoppix papers page, collecting just those who mention MPITB.

(Apr/2009) Willem Vermin has installed MPITB in lisa64, a Top500 11.5TF cluster in SARA Netherlands.
(Mar/2009) Martin Cech, a PelicanHPC user, has posted these timing results in Nabble's PelicanHPC forum.
(Oct/2008) Honoré Tapamo is using MPITB in a Top500 BlueGene/P platform in KTH PDC Sweden. See this thread Jul/08 and this report circa Sep-Oct/2008. See the "MPITB Papers" page for more details.
(Jun/2008) Nils Smeds et al. have ported MPITB to hebb, a Top500 BlueGene/L supercomputer.
(May/2008) Michael has released the new PelicanHPC-1.5.1 which includes MPITB precompiled for Octave-3.0.1 and OpenMPI-1.2.6.
(May/2008) Michael was interviewed for a supercomputation review called TeraFlop (in catalá). Read Michael's section here.
(Jan/2008) Gentur is popularizing Octave/MPITB code in his cluster, see the last 2 messages in this forum.
(Jan/2008) MPITB live at Monash. Find it here, in page 3/7 (linked in the Monash Sun Grid web). Credited to Graham Jenkins (see support staff).
(Jan/2008) Gianvito talks about MPITB in his cluster, in the OctaveWiki > here.
(2/Jan/2008) PelicanHPC is the sequel to P-KPX after v2.8 release. Didn't notice the new Nabble forum name.
(9/Nov/07) Gentur Widyaputra has successfully installed MPITB on his NPACI-Rocks cluster. (see thread)
(26/Sept/07) New ParallelKnoppix forum at Nabble.
(13/Mar/2007) Michael ran 4E6 probits last night!
(16/Nov/06) MPITB considered for inclusion in VL-E POC Release2.
(19/Jun/06) Michael has made a "screencast" of  Octave running in parallel (announcement). The video is a physical proof of the advertised "5 minutes setup". Setup, boot and run the mle_example took 3:45 to Michael. We normal users are expected to spend some 5 minutes :-)
(01/Jun/06) Meeting at ICCS'06 with Breanndán. He patched some MPITB error (see MPI_Unpack.cc around lines 360-365). He has also coauthored 3 MPITB papers with people working in Hydrology, Meteorology and Geosciences.
(Feb/06) MPITB for Octave considered for inclusion in the VL-E POC Environment, see the proposal here. Learn more about VL-E here and here. Breanndán Ó Nualláin is responsible for integrating MPITB and (David Abramson's) Nimrod into VL-E (see attributions in Table 1 here and this talk).
(Feb/06) Gianvito Quarta offered his 64-biproc-nodes ItaniumII cluster to adapt MPITB to IA-64. This is his initial e-mail and this is the summary post.
(2004/05) Dirk Eddelbuettel has added an MPITB item to Quantian's to-do list.
(19/Oct/05) Michael has solved the xterm-window problems and now the Parallel-Knoppix distribution has an MPITB-debug mode, very useful to debug parallel MATLAB applications. See the snaphot here.
(11/Feb/05) Thomas Weber has recompiled MPITB against MPICH-1.2.5.3 and LAM-7.1.1 with the Debian distro. The Makefile will be included in the next MPITB tarball. Michael sent this announcement to help at octave.org.
(11/Jan/05) The Octave wiki includes a mention to MPITB in CategoryCode > CategoryParallel
(10/Jan/05) Michael has finished the paper on econometrics using MPITB: "User-Friendly Parallel Computations with Econometric Examples", see the announcement and preliminary version here. The complete version is here. Also archived at EconPapers / IDEAS.
(May/05) Accepted in Computational Economics, PDF / DOI
(25/Nov/2004) Michael has finished the example, this is the announcement. The ParallelKnoppix live-CD now includes a working example to do a MonteCarlo study in parallel. Michael also announced it here in the Knoppix.net site.
(12/Jan/2005) This is the most updated version of the examples
Michael has built a remastering of the Knoppix live-CD called ParallelKnoppix (see this / this and this and this other announcement). He has also compiled against 2.1.58 / LAM 7.0.6 (see announcement here), and is planning to prepare some example. There is also a Tutorial on ParallelKnoppix (here, alt) tailored with an MPITB example.
Also wholehearted thanks to Michael Creel for his interest and patience. He has also contributed a Makefile for Debian, included in the src subdir.
Wholeheartedly thanks to Christoph L. Spiel for writing the "Da Coda Al Fine" (broken, cached at Google) manual.
And of course to John W. Eaton as well, for making Octave.
And to Paul Kienzle for his advice about licensing nomenclature etc.
 

page built April 2004 Last update: Apr 17th 2009

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